afni.nimh.nih.gov

You should have datasets that end in _warp2std_ns.nii.gz and _warp2std_nsu.nii.gz in your animal warper output directory that correspond to the skull stripped (no skull) and a unifized version of that.

For T2 images to align to a T1 template (or vice versa), you need a cost function that looks for the reverse contrast. The lpc method works well for this. Add the option "-cost lpc" or "-cost lpc+ZZ".